Abilities:
-Charge is great because bosses/adds usually run faster than players. It can be replaced by Boar's speed.
-Thunderstomp is mandatory.
-Last stand is a life-saver CD if anything goes wrong or a boss frenzies, or can be used if pet rotations are in order
-Roar of sacrifice actually serves as a damage reduction CD for the hunter
-Taunt is a tricky ability - it doesn't work on all bosses, but it can be very useful: taunt + FD offers good lead on aggro, making you lose less dps. Besides, some bosses despawn when you FD, so taunt is the only solution to pet switching.-Intervene: I seldom use intervene, so it's better to read about it on http://outdps.com/2011/11/16/hunter-damage-reduction-cooldowns/#more-4803

Abilities:
-Dash is far more interesting than charge
-Serpent swiftness and Bloodthirsty maximize self-heal for your pet.
-Lick your wounds is better used manually near 10% health, because if automatic he will use it at 50% health. It can also be used as a way to gain a lot of aggro.
-Heart of the phoenix allows you to survive an error. It can also be used as a second self-heal (though with aggro drop, so better keep it for times of great need).

Best pets:
Sporebat! (sorry, I just had to say it)

Tenacity:
Turtle/Beetle: best reduction cooldowns. They can be used as soon as possible against easy bosses, or in time with burst damage.
Bear: same overall reduction than turtle, if the boss does linear, physical damage.
Gorilla: 30-second cooldown interrupt.